The excited-state protonation of serotonin and other 5-hydroxy indoles has been studied with a picosecond laser excitation system. It was confirmed that anomalous green emission of these compounds when excited at 280 nm arose from protonation of the excited molecule. Data supporting this conclusion included direct observation of the rise of the green emission after laser excitation, Stern-Volmer plots showing quenching of the normal ultraviolet fluorescence by protons, and chloride ion enhancement of protonation. A systematic characterization of tryptophan dipeptides has been performed with the aim of defining factors which influence the fluorescence of the indole group, which is the major group governing protein fluorescence. It was found that several properties of peptides with N-terminal tryptophan were distinct from those of peptides where tryptophan was C-terminal. Quantum yields, lifetimes, ionization constants, copper binding constants, and absorption spectra supported the idea that there are several non-interconverting forms of these compounds in solution whose relative populations are influenced by indole-protonated amino group interaction.